/*
* RestrictedPartialsParser.java
*
* Copyright (c) 2002-2016 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evomodelxml.continuous;
import dr.evolution.tree.TreeUtils;
import dr.evolution.util.Taxa;
import dr.evolution.util.Taxon;
import dr.evolution.util.TaxonList;
import dr.evomodel.continuous.AbstractMultivariateTraitLikelihood;
import dr.evomodel.continuous.RestrictedPartials;
import dr.evomodel.tree.TreeModel;
import dr.evomodelxml.tree.MonophylyStatisticParser;
import dr.inference.distribution.MultivariateDistributionLikelihood;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* Created by msuchard on 6/4/16.
*/
public class RestrictedPartialsParser extends AbstractXMLObjectParser {
public static final String RESTRICTED_PARTIALS = "restrictedPartials";
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String name = xo.getId();
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
TaxonList taxa = MonophylyStatisticParser.parseTaxonListOrTaxa(xo.getChild(MonophylyStatisticParser.MRCA));
Parameter meanParameter = (Parameter) xo.getElementFirstChild(MultivariateDistributionLikelihood.MVN_MEAN);
Parameter priorSampleSize =
(Parameter) xo.getElementFirstChild(AbstractMultivariateTraitLikelihood.PRIOR_SAMPLE_SIZE);
RestrictedPartials rp = null;
try {
rp = new RestrictedPartials(name, tree, taxa, meanParameter, priorSampleSize);
} catch (TreeUtils.MissingTaxonException e) {
throw new XMLParseException("Unable to find taxa for " + xo.getId());
}
return rp;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(TreeModel.class),
new ElementRule(MonophylyStatisticParser.MRCA, new XMLSyntaxRule[]{
new XORRule(
new ElementRule(Taxon.class, 1, Integer.MAX_VALUE),
new ElementRule(Taxa.class)
)
}),
new ElementRule(MultivariateDistributionLikelihood.MVN_MEAN,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(AbstractMultivariateTraitLikelihood.PRIOR_SAMPLE_SIZE,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
};
public String getParserDescription() {
return "A restricted partials assignment for a set of taxa";
}
public Class getReturnType() {
return RestrictedPartials.class;
}
public String getParserName() {
return RESTRICTED_PARTIALS;
}
}